Egypt's military junta (known as Scaf, short for the Supreme Council of the Armed Forces), has learned to live with the vitriol and revolutionary bravado reaching it from Tahrir Square in the distant city centre.

But this time the "trouble makers" were getting too close for comfort. Abbassia Square, the scene of the latest bloody conflagration in Cairo, is just a stone's throw away from its inner sanctum: the ministry of defence, where Field Marshal Mohamed Hussein Tantawi, the man who took over from his ousted former chief, Hosni Mubarak, has been at the helm for more than 20 years.

The square – close to another student hotbed of vocal opposition to the military, the campus of Ein Shams university – looked like a battlefield. Strewn everywhere were stones and metal bars pulled out of traffic fences to use as weapons in the battles that raged during the past few days.

More tellingly, several rows of troops stood behind barbed wire and next to armoured cars and tanks shielding the heavily fortified ministry of defence to prevent the protesters from reaching their goal. It looked like Scaf was under siege.

A young bearded protester shouted in a loudspeaker: "Tahrir Square has become a Hyde Park Speakers' Corner, come here, the revolution is here." It was not a huge crowd, but, despite repeated vicious attacks by thugs, they had stood their ground and were being joined by other groups angered by the death toll.

Violence against peaceful protesters – like at the height of the uprising that toppled Mubarak last year – has again made people forget their ideological differences.

The Abbassia clash was a bloodbath waiting to happen. Previous attempts to march on the ministry of defence last year by leftist and liberal youths were beaten back by the brutish military police. They were helped in their violent repression then, like now, by machete-wielding thugs. They were also helped by the fact that the radical youth were on their own. Back then, the vastly numerous and better organised Islamists were still enjoying their brief love affair with the military.

From the moment the Salafi crowds – followers of a demagogue militant preacher turned presidential candidate, Hazem Abu Ismail – decided to march on to the ministry of defence in protest against the decision to disqualify their leader in the presidential race, it was only a matter of time. They were eventually joined by an assortment of youth groups, all united in their hatred of military rule and profound suspicion of the soldiers' endgame.

The military's insistence that the violence and deaths were not their fault infuriated everybody. Islamists and secular politicians were united in laying the blame squarely on Scaf and the way it has bungled the country's transition to civilian rule.

In all previous confrontations, the military blamed the deaths on a "third party" – sometimes in the face of overwhelming evidence to the contrary. This time in Abbassia, some of the attackers may very well have been local residents and shopkeepers concerned about their livelihood. But there is no doubt in many people's minds that the lethal onslaught came from hired thugs or military in plainclothes (now bizarrely referred to as "the army's militia"). The use of hired thugs was and still is common practice to intimidate opponents, to infiltrate and break up demonstrations.

A year ago, "down with military rule" was the slogan of a fringe group, The Revolutionary Socialists. Today, it has become adopted by almost all activists, including the Islamists, the military's erstwhile friends.

Is the crunch moment approaching? The final showdown that many feared and just as many wanted to make a clean break with the Mubarak regime by forcing Tantawi and his men out. Perhaps.

The problem is who will take over. The political and constitutional tracks have hit an impasse. There's still no agreement on the criteria to select the constituent assembly that will draft the new constitution. Although the presidential election is due in three weeks, a president without a new constitution could land the country in a legitimacy crisis or with a president wielding Mubarak's absolute powers – something that no one wants.

And the political class that is supposed to take over from Scaf and replace the old nomenklatura is fractious and riven by profound disagreements.

One thing is certain though, Egypt after the Abbassia clashes is edgy and rebellious, and the junta's token gesture to its opponents – an offer to step down early (but only if a president is elected by an absolute majority) – is just that.

The moral of this latest bloody interlude is that the military seems to have failed to learn the lesson from Mubarak. It is still pinning its hopes on turning the "average Egyptian" against the revolution. It may have scored some success, but only just. It's true, some of the Abbassia residents hated the protesters. So did the residents around Tahrir Square over a year ago.

The problem is that Scaf's greatest asset, Mr Average, by his very nature, does not drive history, because he defends the status quo. And he, like the calcified military junta, appears very much out of touch with Egypt's own zeitgeist.

Throughout the past year, Abbassia was the favourite haunt of the pro-army and pro-Mubarak crowds – today it appears set to become another Tahrir Square.